Yes, autophagy is selective. That's the main selling point of long duration fasting. But it's only half useful. You have to go back to regular eating with a balanced diet, otherwise you don't get as much benefits as you could since reconstruction needs quality building blocks.
It will always eat a bit of it, even sane muscle, the process is not perfect. But old cells and sick cells are prioritized. That's one reason it has benefits in combination with chemo therapy : the body will target the cancer cells. Not only those, but it's enough to help.
Same with weak joints, old muscle bruises, etc.
But again, eating properly after the fast is important to let the body rebuild what it destroyed.
I haven't read any study on brain cells specifically. My guess would be that the mechanism is the same and is not locally different according to the different body parts but i can't be sure.
